title: Analysis of DNA methylation in FFPE tissues using the MethyLight technology.
abstract: Novel biomarkers are sought after by mining DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues. Such tissues offer the great advantage of often having complete clinical data (including survival), as well as the tissues are amenable for laser microdissection targeting specific tissue areas. Downstream analysis of such DNA includes mutational screens and methylation profiling. Screening for mutations by sequencing requires a significant amount of DNA for PCR and cycle sequencing. This is self-inhibitory if the gene screened has a large number of exons. Profiling DNA methylation using the MethyLight technology circumvents this problem and allows for the mining of several biomarkers from DNA extracted from a single microscope slide of the tissue of interest. We describe in this chapter a detailed protocol for MethyLight and its use in the determination of CpG Island Methylator Phenotype status in FFPE colorectal cancer samples.
authors.affiliation: King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Ashraf
authors.initials: A
authors.lastname: Dallol
authors.forename: Waleed
authors.initials: W
authors.lastname: Al-Ali
authors.forename: Amina
authors.initials: A
authors.lastname: Al-Shaibani
authors.forename: Fahd
authors.initials: F
authors.lastname: Al-Mulla
mesh_terms: D001483:Base Sequence; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000302:isolation & purification; D019175:DNA Methylation / Q000235:genetics*; D017931:DNA Primers / Q000378:metabolism; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D007335:Insulin-Like Growth Factor II / Q000235:genetics; D008780:Methyltransferases / Q000378:metabolism; D008969:Molecular Sequence Data; D016612:Paraffin Embedding / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011401:Promoter Regions, Genetic / Q000235:genetics; D013447:Sulfites; D016707:Tissue Fixation / Q000379:methods*
chemical_list: D017931:DNA Primers; D013447:Sulfites; D005557:Formaldehyde; D007335:Insulin-Like Growth Factor II; D004247:DNA; D008780:Methyltransferases; C009279:sodium bisulfite